+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14998 | |||||||||
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Title | VWF Tubules of D1D2 and D'D3A1 domains | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / integrin binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Javitt G / Fass D | |||||||||
Funding support | Israel, 1 items
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Citation | Journal: Blood / Year: 2022 Title: Assembly of von Willebrand factor tubules with in vivo helical parameters requires A1 domain insertion. Authors: Gabriel Javitt / Noa Yeshaya / Lev Khmelnitsky / Deborah Fass / Abstract: The von Willebrand factor (VWF) glycoprotein is stored in tubular form in Weibel-Palade bodies (WPBs) before secretion from endothelial cells into the bloodstream. The organization of VWF in the ...The von Willebrand factor (VWF) glycoprotein is stored in tubular form in Weibel-Palade bodies (WPBs) before secretion from endothelial cells into the bloodstream. The organization of VWF in the tubules promotes formation of covalently linked VWF polymers and enables orderly secretion without polymer tangling. Recent studies have described the high-resolution structure of helical tubular cores formed in vitro by the D1D2 and D'D3 amino-terminal protein segments of VWF. Here we show that formation of tubules with the helical geometry observed for VWF in intracellular WPBs requires also the VWA1 (A1) domain. We reconstituted VWF tubules from segments containing the A1 domain and discovered it to be inserted between helical turns of the tubule, altering helical parameters and explaining the increased robustness of tubule formation when A1 is present. The conclusion from this observation is that the A1 domain has a direct role in VWF assembly, along with its known activity in hemostasis after secretion. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14998.map.gz | 121.1 MB | EMDB map data format | |
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Header (meta data) | emd-14998-v30.xml emd-14998.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_14998.png | 52.6 KB | ||
Others | emd_14998_additional_1.map.gz emd_14998_half_map_1.map.gz emd_14998_half_map_2.map.gz | 122.1 MB 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14998 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14998 | HTTPS FTP |
-Validation report
Summary document | emd_14998_validation.pdf.gz | 926.1 KB | Display | EMDB validaton report |
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Full document | emd_14998_full_validation.pdf.gz | 925.7 KB | Display | |
Data in XML | emd_14998_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_14998_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14998 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14998 | HTTPS FTP |
-Related structure data
Related structure data | 7zwhMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14998.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.2396 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_14998_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14998_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14998_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : VWF tubules of D1D2 and D'D3A1 domains
Entire | Name: VWF tubules of D1D2 and D'D3A1 domains |
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Components |
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-Supramolecule #1: VWF tubules of D1D2 and D'D3A1 domains
Supramolecule | Name: VWF tubules of D1D2 and D'D3A1 domains / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: von Willebrand factor
Macromolecule | Name: von Willebrand factor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 131.7835 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MIPARFAGVL LALALILPGT LCAEGTRGRS STARCSLFGS DFVNTFDGSM YSFAGYCSYL LAGGCQKRSF SIIGDFQNGK RVSLSVYLG EFFDIHLFVN GTVTQGDQRV SMPYASKGLY LETEAGYYKL SGEAYGFVAR IDGSGNFQVL LSDRYFNKTC G LCGNFNIF ...String: MIPARFAGVL LALALILPGT LCAEGTRGRS STARCSLFGS DFVNTFDGSM YSFAGYCSYL LAGGCQKRSF SIIGDFQNGK RVSLSVYLG EFFDIHLFVN GTVTQGDQRV SMPYASKGLY LETEAGYYKL SGEAYGFVAR IDGSGNFQVL LSDRYFNKTC G LCGNFNIF AEDDFMTQEG TLTSDPYDFA NSWALSSGEQ WCERASPPSS SCNISSGEMQ KGLWEQCQLL KSTSVFARCH PL VDPEPFV ALCEKTLCEC AGGLECACPA LLEYARTCAQ EGMVLYGWTD HSACSPVCPA GMEYRQCVSP CARTCQSLHI NEM CQERCV DGCSCPEGQL LDEGLCVEST ECPCVHSGKR YPPGTSLSRD CNTCICRNSQ WICSNEECPG ECLVTGQSHF KSFD NRYFT FSGICQYLLA RDCQDHSFSI VIETVQCADD RDAVCTRSVT VRLPGLHNSL VKLKHGAGVA MDGQDVQLPL LKGDL RIQH TVTASVRLSY GEDLQMDWDG RGRLLVKLSP VYAGKTCGLC GNYNGNQGDD FLTPSGLAEP RVEDFGNAWK LHGDCQ DLQ KQHSDPCALN PRMTRFSEEA CAVLTSPTFE ACHRAVSPLP YLRNCRYDVC SCSDGRECLC GALASYAAAC AGRGVRV AW REPGRCELNC PKGQVYLQCG TPCNLTCRSL SYPDEECNEA CLEGCFCPPG LYMDERGDCV PKAQCPCYYD GEIFQPED I FSDHHTMCYC EDGFMHCTMS GVPGSLLPDA VLSSPLSHRS KRSLSCRPPM VKLVCPADNL RAEGLECTKT CQNYDLECM SMGCVSGCLC PPGMVRHENR CVALERCPCF HQGKEYAPGE TVKIGCNTCV CRDRKWNCTD HVCDATCSTI GMAHYLTFDG LKYLFPGEC QYVLVQDYCG SNPGTFRILV GNKGCSHPSV KCKKRVTILV EGGEIELFDG EVNVKRPMKD ETHFEVVESG R YIILLLGK ALSVVWDRHL SISVVLKQTY QEKVCGLCGN FDGIQNNDLT SSNLQVEEDP VDFGNSWKVS SQCADTRKVP LD SSPATCH NNIMKQTMVD SSCRILTSDV FQDCNKLVDP EPYLDVCIYD TCSCESIGDC ACFCDTIAAY AHVCAQHGKV VTW RTATLC PQSCEERNLR ENGYECEWRY NSCAPACQVT CQHPEPLACP VQCVEGCHAH CPPGKILDEL LQTCVDPEDC P |
-Macromolecule #2: von Willebrand factor
Macromolecule | Name: von Willebrand factor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.882568 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PPLHDFYCSR LLDLVFLLDG SSRLSEAEFE VLKAFVVDMM ERLRISQKWV RVAVVEYHDG SHAYIGLKDR KRPSELRRIA SQVKYAGSQ VASTSEVLKY TLFQIFSKID RPEASRITLL LMASQEPQRM SRNFVRYVQG LKKKKVIVIP VGIGPHANLK Q IRLIEKQA ...String: PPLHDFYCSR LLDLVFLLDG SSRLSEAEFE VLKAFVVDMM ERLRISQKWV RVAVVEYHDG SHAYIGLKDR KRPSELRRIA SQVKYAGSQ VASTSEVLKY TLFQIFSKID RPEASRITLL LMASQEPQRM SRNFVRYVQG LKKKKVIVIP VGIGPHANLK Q IRLIEKQA PENKAFVLSS VDELEQQRDE IVSYLCDLAP E |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 5.9 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.6 Å Applied symmetry - Helical parameters - Δ&Phi: 83.1 ° Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral) Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 739073 |
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Startup model | Type of model: INSILICO MODEL / In silico model: Helical Ab initio |
Final angle assignment | Type: NOT APPLICABLE |